GET_PHYLOMARKERS_v2.1.0_2024-03-31

This release (v2.1.0, 2024-03-31) contains new features, significant code improvements, binary updates, and some bug fixes

New features

1. Implemented the maximal matched-pairs tests to asses violations of the data to the Stationarity, Reversibility, and Homogeneity (SRH) assumptions made by maximum-likelihood phylogenetic models, as implemented in iqtree2.

2. run_get_phylomarkers_pipeline.sh now calls the C binary ASTRAL-IV instead of the older java ASTRAL-III jar to estimate a species tree using as input the filtered gene trees estimated by iqtree2 or FastTree from the core-genome clusters computed by get_homologues.

3. The main script run_get_phylomarkers_pipeline.sh runs under Bash's unofficial strict mode set -euo pipefail. Additionally, the code was thoroughly revised, improving the code layout and using a more idiomatic and modern bash syntax.

Updated external programs

• ASTRAL-IV replaces ASTRAL-III to estimate the concatenation-free species tree
• IQ-TREE v.2.3.1

Updated scripts and library code

• run_get_phylomarkers_pipeline.sh
• run_kdetrees.R
• lib/get_phylomarkers_fun_lib

Docker image

The distribution contains a Dockerfile used to build the Docker image ready to pull from Docker Hub. On Dockerhub, you will find detailed instructions on installing and configuring the Docker client on your machine, pulling the latest image, and running the containerized instance of the GET_PHYLOMARKERS pipeline.